Transcript Tape Measure Protein (TMP)

Tape Measure Protein (TMP)
Structural
proteins
- determinant of phage tail length
- gene length determines length of
tail
Is used and uses proteins during tail
assembly; therefore, critical during
assembly process [1, 2]
Katherine Figueroa
Motifs Determined
Three motifs within set of 14
mycobacteriophages [4]
Proteins that have motif 3 have
peptidoglycan hydrolysing activity [1]
Easing efficient infection and DNA injection
Goal of Experiment
To simulate the three motifs of Pedulla et al.
in BioBIKE and localize motif 3 in proteins
of mycobacteriophages
Motif 1
Motif 2
Motif 3
- Gathered tmps in mycobacteriophages using protein categories in subsystems [5]
- made list sequences similar to the tmp of mycobacteriophage TM4
- scanned list of sequences similar to TM4 tmp applying defined motifs
1, 2, and 3
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Determined what a bad result and good result looked like
Proceeded to apply motif 3 to the proteins of mycobacteriophages
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- tougher than I thought
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- still defining function to search for motif 3 in the proteins of all mycobacteriophages
- Instead created a subset consisting of 14 mycobacteriophages
Results
References
[1] Piuri, Mariana and Hatfull, Graham F. 2006. A peptidoglycan
hydrolase motif within the mycobacteriophage TM4 tape
measure protein promotes efficient infection of stationary
phase cells. Molecular Microbiology;62(6): 1569-1585.
[2] Katsura, I., and Hendrix, R.W. (1984) Length determination in
bacteriophage lambda tails. Cell 39:691-698.
[3] Pedulla, M.L., Ford, M.E., Houtz, J.M., Karthikeyan, T., Wadsworth,
C., Lewis, J.A., et al. (2003) Origins of highly mosaic
mycobacteriophage genomes. Cell 113: 171-182.
[4] Mycobacteriophage Database
[5] Elhai, J., Arnaud, T., Massar, J.P., Myers, J. K., Travers, M., Casey,
J., Slupesky, M., Shrager, J. (2009) BioBIKE: a web-based,
programmable, integrated biological knowledge base. Nucleic
Acids Research 37: p.w28-w32.
Tandem Repeats of Similar
Cluster Phages
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Found the amino acid sequence’s of the following phages:
B1 Sub cluster – Scoot, Abu, & Chah
B2 Sub Cluster - Ares
B3 Sub Cluster - Akoma
B4 Sub Cluster - Fredrick
A2 Sub Cluster - L5 & D29
Sub Cluster B1 Motif
Sub Cluster Block Motifs
Alligned all sub slusters to look
for tandem repeats
Clustal Omega was used to find any similar tandem repeats within Sub
Clusters B1, B2, B3, B4, & A2
Phylogenic Relationship
Results
• Unable to find any similar tandem repeats within sub clusters B1,
B2, B3, B4, and A2
• Results indicate that within sub cluster B, many identical amino
acids were found in the same position within the tmp
• Sub Cluster A2 and B1-4 did show some similar over lapping
amino acid sequences in similar positions within their tmps
• Phylogenic tree shows that sub clusters A2 and B1-4 do share a
common ancestry in their tmp
References
1.The evolution of the tape measure protein: units, duplications and losses:
Belcaid M, Bergeron A, Poisson G. BMC Bioinformatics. 2011 Oct 5;12 Suppl
9:S10. doi: 10.1186/1471-2105-12-S9S10.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271669/
2.Length Determination in Bacteriophage Lambda Tails. Katsura, I and
Hendrix, R. Cell, Vol . 39, 691-698, December 1984. http://ac.elscdn.com/0092867484904768/1-s2.0-0092867484904768main.pdf?_tid=46972fa4-9c69-11e2-b6bc00000aab0f26&acdnat=1364998854_34031474c286eed57d3f1aadfd1a1d92
3.Mechanism of Length Determination in Bacteriophage Lambda Tail.
Katsura, Isao. Department of Biology, College of Arts and Sciences, The
University of Tokyo, Meguro-ku, Tokyo 153, Japan. Adv. Biophys., Vol. 26, pp.
1-18 (1990).